Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate WP_057506874.1 ABB28_RS01185 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_001431535.1:WP_057506874.1 Length = 583 Score = 637 bits (1643), Expect = 0.0 Identities = 330/587 (56%), Positives = 410/587 (69%), Gaps = 11/587 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+H+CG ++E+L GQ VTL GW R+ GGV F+D+RD EG+ QV + D AE FA A Sbjct: 1 MRTHFCGLVDETLIGQTVTLAGWTDVARNQGGVCFIDLRDHEGIVQVTVEVDNAEVFAVA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + E V+++ G VR R A N MA+G +EV+ + VLN+A P P + + GE Sbjct: 61 ASLGYEDVLQVEGVVRARH--AVNDKMATGKVEVIATAITVLNKAA--PLPFHAHENPGE 116 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 ETRL+YR++DLRRPEM + R ++ ++RR+LD+ GF D+ETPIL + TPEGARD+LV Sbjct: 117 ETRLKYRYLDLRRPEMQRMQRTRIKLVQALRRHLDERGFQDIETPILTKATPEGARDFLV 176 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 P+R +PG F+ALPQSPQLFKQ+LMVAGFDRYYQIA+CFRDE LRADRQ EFTQ+D+E +F Sbjct: 177 PARMHPGEFYALPQSPQLFKQILMVAGFDRYYQIARCFRDEALRADRQLEFTQLDMEFAF 236 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFD-EFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 + E D+ E M+R +FKEV+DVE D FP M + EAMRRYGSDKPDLRI LELVDVA+ Sbjct: 237 VREQDVQDFVEDMIRGIFKEVVDVELDARFPRMTWAEAMRRYGSDKPDLRIALELVDVAE 296 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 +K EF VF+ AND GRVAALR+PG A++ R QID+Y YGAKGLAYIKV E Sbjct: 297 LVKSSEFPVFTAAANDADGRVAALRIPGGATLSRKQIDEYAAHAAKYGAKGLAYIKVGEN 356 Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420 + + SPI KF E +L VGA GDIVFFGA V D +GALR+K G D Sbjct: 357 GE----ISSPIQKFFSEDGFAALLAHVGAGKGDIVFFGAGGYNKVSDFMGALRLKAGKDF 412 Query: 421 KLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTP-AELEANPGAALSRAYDMV 478 L+ WAP+WV DFPMFE +++ ALHHPFT+P A+L + A+SR YDMV Sbjct: 413 GLVADGWAPLWVTDFPMFEWDEEAQRYVALHHPFTAPAVDDIADLRTHAKTAVSRGYDMV 472 Query: 479 LNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDR 538 LNG E+GGGSIRIH MQ AVF +LGID E KFGFLLDAL YGAPPHGG+AFG+DR Sbjct: 473 LNGNEIGGGSIRIHRPDMQSAVFELLGIDAEEARAKFGFLLDALNYGAPPHGGIAFGIDR 532 Query: 539 LVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLR 585 + LM G SIR+VI FPKT A +MT AP + L E+HI++R Sbjct: 533 IAALMAGTESIRDVIPFPKTTGAQCLMTDAPSPIADAQLAEVHIQVR 579 Lambda K H 0.321 0.140 0.411 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1044 Number of extensions: 45 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 591 Length of database: 583 Length adjustment: 37 Effective length of query: 554 Effective length of database: 546 Effective search space: 302484 Effective search space used: 302484 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory